rs199422262

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP5BP4

The NR_001566.1(TERC):​n.48A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).

Frequency

Genomes: not found (cov: 32)

Consequence

TERC
NR_001566.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: 2.92
Variant links:
Genes affected

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 3-169765013-T-C is Pathogenic according to our data. Variant chr3-169765013-T-C is described in ClinVar as [Pathogenic]. Clinvar id is 39297.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-169765013-T-C is described in Lovd as [Pathogenic].
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.38). . Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TERCNR_001566.1 linkuse as main transcriptn.48A>G non_coding_transcript_exon_variant 1/1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
Telomerase-vertENST00000363312.1 linkuse as main transcriptn.35A>G non_coding_transcript_exon_variant 1/16
TERCENST00000602385.1 linkuse as main transcriptn.48A>G non_coding_transcript_exon_variant 1/16

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
0
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Dyskeratosis congenita, autosomal dominant 1 Pathogenic:1
Pathogenic, no assertion criteria providedcurationGeneReviewsMay 10, 2012- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.38
CADD
Benign
21
DANN
Benign
0.65
RBP_binding_hub_radar
0.97
RBP_regulation_power_radar
2.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs199422262; hg19: chr3-169482801; API